All members of the Chlamydiae, including Waddlia chondrophila share the same unique intracellular development cycle, which is the focus of this work in the search for anti-chlamydial targets and drugs. Strategies using high throughput screening, genetic complementation, and metabolomics were explored to investigate and try to block the W. chondrophila development cycle. First, a generic high throughput screening procedure was developed in a heterologous system, Escherichia coli, to search for inhibitors of chlamydial transcription factors. Then, the function of DksA, a transcription factor, was investigated by genetic complementation of E. coli and Pseudomonas aeruginosa mutants. Finally, metabolomics was adopted to observe changes in metabolites associated with progress through the chlamydial developmental cycle. It revealed the presence of putative novel metabolites differentially expressed in the various stages. Altogether, the results of this work present putative new therapeutic approaches to understand and circumvent the infection process of this pathogen.